Hello Hagen, Attachments are screened by the monitor program and I didn't request a copy in time today. However, I have deduced that the target species is /C.elegens/ May 2008 (ce6) assembly and the track either "Nucleosome" or one of the derivatives (with variable stringencies applied). The answers should address this set of tracks and actually most tracks in general, but please write back if I don't answer your questions completely.
1) Yes, with the BED format output one of the options is 1 record per line is for each read. Depending on which table you are retrieving, the Table browser may be able to export the data. The limit for the TB output is 100k lines. For tables with more data, either export the data per chromosome using the TB, use the public mySQL server, or ftp the file from the Downloads server (species -> assembly -> Annotation database -> table name = file name.txt.gz). The data for this track is in BED format in the database and therefore the files in Downloads are also BED format. Ftp instructions: http://genome.ucsc.edu/FAQ/FAQdownloads#download1 Public mySQL server: http://genome.ucsc.edu/FAQ/FAQdownloads#download29 2) Again, yes, column 5 is score, which for this track is the collapsed depth of reads, grouped by starting position, as documented on the track description page in the section "Display Conventions and Configuration". BED format is described here: http://genome.ucsc.edu/FAQ/FAQformat#format1 Some stats and example SQL query for summarizing score values: unix$ hgsql ce6 mysql> select count(*), score from nucleosomeControl group by score; +----------+-------+ | count(*) | score | +----------+-------+ | 18614626 | 1 | | 5371783 | 2 | | 2243522 | 3 | | 1107780 | 4 | | 603639 | 5 | | 353237 | 6 | more .... | 1 | 345 | +----------+-------+ 193 rows in set (0.00 sec) Thank you for your patience today while we worked out an answer and please write back if you have questions or would like more help, Jennifer Jackson UCSC Genome Bioinformatics Group Hagen Tilgner wrote: > Dear UCSC developpers and users, > > I have two questions that hopefully require only a short "yes". > > 1) I downloaded nucleosome reads from the table-browser (see > README_download.png for a screenshot of what I exactly did) from the > valouev et al publication. Upon hitting "get output" I get to a page > (see makeSurecorrect.png for a screenshot) that asks me whether I want > 1 record per gene, exon, etc. All I want is 1 bed-line per read of the > experiment genome wide, independently of any annotation. Is this what > I get when hitting "get BED" as in the attached png ? > > 2) I assume that column 5 in the resulting bed-file gives me the > number of times this read was observed. Am I right ? > > I would really appreciate your help > Hagen > ------------------------------------------------------------------------ > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
